Multiple sequence alignment - TraesCS7B01G398500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G398500 chr7B 100.000 3471 0 0 1 3471 664945957 664949427 0.000000e+00 6410
1 TraesCS7B01G398500 chr7B 97.898 3473 69 3 1 3471 666622404 666618934 0.000000e+00 6006
2 TraesCS7B01G398500 chr7B 97.892 2609 50 4 1 2608 379917863 379915259 0.000000e+00 4508
3 TraesCS7B01G398500 chr3B 98.071 3473 62 4 1 3471 734220748 734224217 0.000000e+00 6037
4 TraesCS7B01G398500 chr5B 97.581 3473 62 10 1 3471 353924416 353927868 0.000000e+00 5928
5 TraesCS7B01G398500 chr5B 97.495 3473 65 10 1 3471 18190431 18186979 0.000000e+00 5912
6 TraesCS7B01G398500 chr5B 96.736 3493 66 7 1 3471 123793381 123789915 0.000000e+00 5775
7 TraesCS7B01G398500 chr5B 96.954 3447 80 8 1 3425 34299685 34296242 0.000000e+00 5760
8 TraesCS7B01G398500 chr5B 94.026 1222 29 4 2271 3471 514054862 514053664 0.000000e+00 1812
9 TraesCS7B01G398500 chr4B 97.641 2755 57 4 1 2749 522410190 522407438 0.000000e+00 4721
10 TraesCS7B01G398500 chr3D 93.453 2902 129 18 1 2874 581478979 581476111 0.000000e+00 4250
11 TraesCS7B01G398500 chr6B 87.477 1613 113 31 1312 2873 77323085 77324659 0.000000e+00 1777
12 TraesCS7B01G398500 chr6B 95.230 587 27 1 2886 3471 77324753 77325339 0.000000e+00 928
13 TraesCS7B01G398500 chr4A 96.422 587 20 1 2886 3471 692373579 692374165 0.000000e+00 966
14 TraesCS7B01G398500 chr4A 87.848 395 18 5 2346 2734 692372915 692373285 1.480000e-118 436
15 TraesCS7B01G398500 chr4A 90.233 215 20 1 2661 2874 692373272 692373486 2.640000e-71 279


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G398500 chr7B 664945957 664949427 3470 False 6410.000000 6410 100.0000 1 3471 1 chr7B.!!$F1 3470
1 TraesCS7B01G398500 chr7B 666618934 666622404 3470 True 6006.000000 6006 97.8980 1 3471 1 chr7B.!!$R2 3470
2 TraesCS7B01G398500 chr7B 379915259 379917863 2604 True 4508.000000 4508 97.8920 1 2608 1 chr7B.!!$R1 2607
3 TraesCS7B01G398500 chr3B 734220748 734224217 3469 False 6037.000000 6037 98.0710 1 3471 1 chr3B.!!$F1 3470
4 TraesCS7B01G398500 chr5B 353924416 353927868 3452 False 5928.000000 5928 97.5810 1 3471 1 chr5B.!!$F1 3470
5 TraesCS7B01G398500 chr5B 18186979 18190431 3452 True 5912.000000 5912 97.4950 1 3471 1 chr5B.!!$R1 3470
6 TraesCS7B01G398500 chr5B 123789915 123793381 3466 True 5775.000000 5775 96.7360 1 3471 1 chr5B.!!$R3 3470
7 TraesCS7B01G398500 chr5B 34296242 34299685 3443 True 5760.000000 5760 96.9540 1 3425 1 chr5B.!!$R2 3424
8 TraesCS7B01G398500 chr5B 514053664 514054862 1198 True 1812.000000 1812 94.0260 2271 3471 1 chr5B.!!$R4 1200
9 TraesCS7B01G398500 chr4B 522407438 522410190 2752 True 4721.000000 4721 97.6410 1 2749 1 chr4B.!!$R1 2748
10 TraesCS7B01G398500 chr3D 581476111 581478979 2868 True 4250.000000 4250 93.4530 1 2874 1 chr3D.!!$R1 2873
11 TraesCS7B01G398500 chr6B 77323085 77325339 2254 False 1352.500000 1777 91.3535 1312 3471 2 chr6B.!!$F1 2159
12 TraesCS7B01G398500 chr4A 692372915 692374165 1250 False 560.333333 966 91.5010 2346 3471 3 chr4A.!!$F1 1125

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
608 613 1.614996 TCGTGTTGGCCAATTGACAT 58.385 45.0 23.66 0.00 0.00 3.06 F
1373 1380 1.501169 CTGAACGAGATGTGCACACA 58.499 50.0 24.37 12.72 46.44 3.72 F
1655 1662 1.243342 CGACTTGGGCCATCAAGCAA 61.243 55.0 18.52 5.78 45.77 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1482 0.898320 ACTCTCATCCCTTGGTGTCG 59.102 55.000 0.0 0.0 0.00 4.35 R
2273 2280 1.933181 CTGTTGCAAGACAAGACGACA 59.067 47.619 0.0 0.0 39.50 4.35 R
2726 2910 3.915437 AACAGCAAAACGTAAGGATGG 57.085 42.857 0.0 0.0 46.39 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
608 613 1.614996 TCGTGTTGGCCAATTGACAT 58.385 45.000 23.66 0.00 0.00 3.06
680 685 1.832219 CATCATTGGCTCCGAGGGA 59.168 57.895 0.00 0.00 0.00 4.20
707 713 2.106166 GGAGTAGTATCCCTCCAGACGA 59.894 54.545 0.00 0.00 45.47 4.20
744 750 3.264897 CAGCACGCCCGAGCATAC 61.265 66.667 12.22 0.00 39.83 2.39
1082 1088 3.202906 CCGAGAAAAACAAGACACCTCA 58.797 45.455 0.00 0.00 0.00 3.86
1373 1380 1.501169 CTGAACGAGATGTGCACACA 58.499 50.000 24.37 12.72 46.44 3.72
1475 1482 1.620323 ACAATTTGGGAGAAGGCAAGC 59.380 47.619 0.78 0.00 0.00 4.01
1655 1662 1.243342 CGACTTGGGCCATCAAGCAA 61.243 55.000 18.52 5.78 45.77 3.91
1782 1789 3.062042 CGTTACCGGTTGAAGCTAAAGT 58.938 45.455 15.04 0.00 0.00 2.66
1853 1860 7.554835 GGGTATATGGACTTCAATGTACAAACA 59.445 37.037 0.00 0.00 40.69 2.83
2120 2127 8.390921 ACCTCTATTCAAAAACCTCCATCTTTA 58.609 33.333 0.00 0.00 0.00 1.85
2134 2141 6.263168 CCTCCATCTTTACACACTTTTGACTT 59.737 38.462 0.00 0.00 0.00 3.01
2135 2142 7.444183 CCTCCATCTTTACACACTTTTGACTTA 59.556 37.037 0.00 0.00 0.00 2.24
2273 2280 0.171903 CCGGGACAATAGACGTCGTT 59.828 55.000 10.46 6.66 34.04 3.85
2309 2316 3.808728 CAACAGGAACAACAAGAGGAGA 58.191 45.455 0.00 0.00 0.00 3.71
2571 2656 0.887387 TGGCGTGAACTTTGCTACCC 60.887 55.000 0.00 0.00 0.00 3.69
2726 2910 3.609807 GCTGTTATGCTTAGTTTTGCTGC 59.390 43.478 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
333 338 2.202557 CATACCGCTCGTCGCACA 60.203 61.111 0.00 0.00 39.08 4.57
608 613 1.072505 GAGGCTCGGGGAAAACACA 59.927 57.895 0.00 0.00 0.00 3.72
744 750 3.430374 CCCTCGTTAACAGATACCACAGG 60.430 52.174 6.39 0.79 0.00 4.00
1082 1088 0.548031 ATGTGCGACCCATCCTTCAT 59.452 50.000 0.00 0.00 0.00 2.57
1373 1380 2.586425 CCCGCCAAATATTCCTGTCAT 58.414 47.619 0.00 0.00 0.00 3.06
1405 1412 5.200368 TCGACAGCATAGAAGCATATCAA 57.800 39.130 0.00 0.00 36.85 2.57
1475 1482 0.898320 ACTCTCATCCCTTGGTGTCG 59.102 55.000 0.00 0.00 0.00 4.35
1655 1662 6.742644 GATTCCACAAATCTATCCACTCGGAT 60.743 42.308 0.00 0.00 43.23 4.18
1782 1789 1.070105 CCGAACAGTTCCAACCGGA 59.930 57.895 9.46 0.00 40.60 5.14
1794 1801 3.146066 CCAACTCTTCCAATTCCGAACA 58.854 45.455 0.00 0.00 0.00 3.18
1853 1860 1.760613 TGTGTCCCTTCGTTGTCTCTT 59.239 47.619 0.00 0.00 0.00 2.85
1982 1989 1.005805 TGCAATAACTCCATGCCCTGT 59.994 47.619 0.00 0.00 39.31 4.00
2273 2280 1.933181 CTGTTGCAAGACAAGACGACA 59.067 47.619 0.00 0.00 39.50 4.35
2309 2316 2.502295 CTCTGGCTCTTCTTGCAGTTT 58.498 47.619 0.00 0.00 0.00 2.66
2448 2482 5.373812 TCACTTCTTCCTTCCTCTTTTGT 57.626 39.130 0.00 0.00 0.00 2.83
2571 2656 4.606961 AGTGCAAATTAAACACAAGTCCG 58.393 39.130 0.00 0.00 36.76 4.79
2726 2910 3.915437 AACAGCAAAACGTAAGGATGG 57.085 42.857 0.00 0.00 46.39 3.51
2918 3215 8.723311 ACGAATTTGAGACCGTTTATTTATGAA 58.277 29.630 0.00 0.00 30.41 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.